Biology subjects

Clark, C. J.

Publications and source records attributed to Clark, C. J..

3 recordsLinked to original sources

bioRxiv2024

Estimating wingbeat frequency on hummingbirds by using a no-labeling learning computer vision approach

SynopsisWingbeat frequency estimation is an important aspect for the study of avian flight, energetics, and behavioral patterns, among others. Hummingbirds, in particular, are ideal subjects to test a method for this estimation due to their fast wing motions and unique aerodynamics, which results from their ecological diversification, adaptation to high-altitude environments, and sexually selected displays. Traditionally, wingbeat frequency measurements have been done via "manual" image/sound processing. In this study, we present an automated method to detect, track, classify, and monitor hummingbirds in high-speed video footage, accurately estimating their wingbeat frequency using computer vision techniques and signal analysis. Our approach utilizes a zero-shot learning algorithm that eliminates the need for labeling during training. Results demonstrate that our method can produce automated wingbeat frequency estimations with minimal supervision, closely matching those performed by trained human observers. This comparison indicates that our method can, in some scenarios, achieve low or zero error compared to a human, making it a valuable tool for flight analysis. Automating video analysis can assist wingbeat frequency estimation by reducing processing time and, thus, lowering barriers to analyze biological data on fields such as aerodynamics, foraging behavior, and signaling.

bioinformatics↗

bioRxiv2023

Beta-subunit-eliminated eHAP expression (BeHAPe) cells reveal new properties of the cardiac voltage-gated sodium channel

Voltage-gated sodium (NaV) channels drive the upstroke of the action potential and are comprised of a pore-forming -subunit and regulatory {beta}-subunits. The {beta}-subunits modulate the gating, trafficking, and pharmacology of the -subunit. These functions are routinely assessed by ectopic expression in heterologous cells. However, currently available expression systems may not capture the full range of these effects since they contain endogenous {beta}-subunits. To better reveal {beta}-subunit functions, we engineered a human cell line devoid of endogenous NaV {beta}-subunits and their immediate phylogenetic relatives. This new cell line, {beta}-subunit-eliminated eHAP expression cells (BeHAPe), were derived from haploid eHAP cells by engineering inactivating mutations in SCN1B, SCN2B, SCN3B, SCN4B, MPZL1, MPZL2, MPZL3, MPZ and JAML. In diploid BeHAPe cells, the cardiac NaV -subunit, NaV1.5, was highly sensitive to {beta}-subunit modulation and revealed that each {beta}-subunit and even MPZ imparted unique gating properties. Furthermore, combining {beta}1 and {beta}2 with NaV1.5 generated a sodium channel with hybrid properties, distinct from the effects of the individual subunits. Thus, this approach revealed an expanded ability of {beta}-subunits to regulate NaV1.5 activity and can be used to improve the characterization of other /{beta} NaV complexes.

biophysics↗

bioRxiv2022

Tuning aromatic contributions by site-specific encoding of fluorinated phenylalanine residues in bacterial and mammalian cells

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a new group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools will enable deconstruction of biological mechanisms which utilize aromatic-pi interactions in structural and cellular contexts. Statement of SignificanceThe aromatic side-chains of phenylalanine, tyrosine, and tryptophan are crucial for protein function and pharmacology due to their hydrophobic and electrostatic contributions to catalytic centers and ligand-binding pockets. However, few experimental approaches can chemically assess the functional roles of aromatics in cellular environments. The accepted computational method for aromatic interrogation is via serial fluorination, which lacks an experimental correlate in bacterial or mammalian cell systems. We have identified a family of synthetases to encode multiple different types of fluorinated phenylalanine residues in E. coli and HEK cells via nonsense suppression. The efficiency of these synthetases is sufficient to support biochemical characterization and structural determination of proteins with site-specific incorporation of unnatural phenylalanine analogs.

biochemistry↗